City of New Beginings
by mitmee2012
Summary: Months after the demon realm and Jocelyn and Luke's wedding everything seems perfect in Clary's life. She has her best friend, her boyfriend, and her parents on her side. Until she starts getting sick.
1. Chapter 1

First a few side notes: Be forewarned that this story contains City of Heavenly Fire spoilers! So, please please don't complain about them because YOU HAVE BEEN WARNED. Anyways, lets get on with it!

Disclaimer; I do not own. I wish, but no.

In the months after Luke and Jocelyn's wedding Clary began to build her relationship back up with Simon, while trying to still give him some space to find his place with Isabelle. The fact that he was ascending was both scary and exciting at the same time. Simon had been a part of this adventure in Clary's life since it began, but he had always been on the outside, now he was right in the center with her. Jace wasn't so happy that he had to give up some "Clary-time" to the not-so-blood-sucking previous bloodsucker, but it made Clary happy so he dealt with it.

Not only was Simon's ascension a big change, but after months of begging, pleading, compromising, and promising Jocelyn decided to let Clary move into the Institute to advance some of her training. Life seemingly was perfect to Clary, she had everything going her way and everything she could ever want… Until she started throwing up every day like clockwork.

Clary had just woken up and ate breakfast before she went to meet Jace for her training session when all of a sudden she ran to the bathroom to expel her breakfast for the third day in a row. Obviously, shadowhunters weren't impervious to getting sick, but it really wasn't beneficial to get sick right before she had to train. Clary chugged some water and hoped like hell that it would give her at least a little of the energy she needed for this session.

"You're late." Jace said as Clary walked into the room wiping off the water from her mouth.

"I know, sorry. I was getting sick again." She told him, ignoring his annoyed look.

"Again?" He said worriedly, "Maybe we should get you to a doctor.."

"You know as well as I do that we can't do that. Shadowhunters don't go to doctors. I'll call Magnus later. Let's just get through this session." Clary said, brushing off his worries.

Not needing to be told again, Jace got down to business and started coaching Clary on the best ways for her to use her particular skill sets to her advantage. Although, she never did anyways, he stressed the importance of her NEVER going anywhere without her stele. They worked for about an hour and a half before Jace sent her off to go get showered, fed and call Magnus. He was really worried about her, despite her claims that they were fine. He may be the 'badass' but when it came to Clary he was slightly over-protective.

Only to prove to Jace that she was fine and that she wasn't as fragile as she seemed she called Magnus first and asked if he would mind coming over to look her over. He agreed to come over before meeting Alec for their weekly date night, but Clary still had a few hours before he got there so she decided to take a shower and see what Simon was up to. When he didn't answer his phone, she assumed that he was with Isabelle, so she went to find Jace. They needed a little time to be together anyways, they hadn't really had much time alone since their trip to the demon realms and that was MONTHS ago. They squeezed in an hour or so together when they could, which led to many pleasurable and fun-filled moments, but they were few and in between.

Clary found Jace in his room, cleaning the already meticulous space. "Hey" she said peeking around the door.

"Hey yourself." He said smiling as he walked over to her.

"Do you want to watch a movie while I wait for Magnus?" She asked him. Clary had made it her personal mission to educate all of the Lightwoods on the art and wonder of cinema.

"I suppose that I will if I have to." He conceded with a smile. He didn't love sitting around watching movies, but he welcomed the time with his girl.

Clary put in a random movie, since it wasn't likely that they were actually going to watch the movie anyways. She was right. No sooner than Clary had pressed play Jace was climbing to lay on top of her on the couch kissing her as if he hadn't seen her in months rather than an hour. It wasn't like she was complaining though, Clary loved kissing Jace. Their kisses started off sweetly but began to deepen quickly. Jace clearly missed their time alone as much as Clary did. Just as things were really heating up and were heading in the direction that Clary had been craving Alec knocked on the door to Jace's room.

"Uh, guys?" He said sheepishly as a blush creeped into his cheeks. He may have been well over his crush on Jace, but the awkwardness of catching your old crush and parabati in bed with his girlfriend was overwhelming and it seemed to always happen to Alec.

"Yeah?" Jace said, without stopping his trail of kisses down Clary's throat.

"Uh, Magnus is here to see Clary. Soooo, yea. We're in the hall."

"Cock-blocker." Jace called after him.

Clary chuckled as she got up and straightened her clothes to go meet Magnus. For some reason she felt the need to go to this appointment alone and process whatever Magnus found was wrong with her without Jace being overly worried. Clary knew that nothing major was wrong with her that could possibly threaten her life, but she also knew that Jace would worry if Magnus said she had the flu. When Jace got up to walk with her, she gently shook her head at him, causing a perplexed look to cross his face.

"I'll be fine," she said "Plus, it'll only be like twenty minutes and then I'll be yours again."

"Fine." He sighed resigning not to fight her on this.

Clary kissed his cheek and went out to meet Magnus in the hall by her bedroom. Thankfully when Alec saw that Jace wasn't with her, he assumed that Clary wanted to maintain some privacy in her appointment. It's not like Magnus wouldn't tell him later if something was seriously wrong with Clary, even the warlock knew that Clary would try to hide something from the others if she felt it would worry them or cause them stress. That's just the kind of person that she was.

Clary and Magnus headed into her room and shut the door behind them so that Clary could talk to him without everyone overhearing. "So what's wrong biscuit?" he asked.

"I've just been really sick the last few days anytime I eat and Jace was starting to get worried." Clary explained.

"Well, let me see what I feel." Magnus said. Instantly his fingers and arms started to light up blue as he ran them over Clary's perfectly still body. After a few minutes he stopped with a rather perplexed look on his face. Clary thought to herself that he must feel either something was very confusing, or he was trying to figure out how to make something sound okay.

"Um, biscuit," he started, as he blushed. "Have you and Jace, uh, ya know?"

" Well, not that it's any of your business, but yes. We have. And, don't try and trick me into thinking that he gave—" she started as he cut her off.

"He didn't give you anything sweetie. Well, not exactly. But, Clary dear, you're pregnant." He explained rather awkwardly.


	2. Chapter 2

First a few side notes: Be forewarned that this story contains City of Heavenly Fire spoilers! So, please please don't complain about them because YOU HAVE BEEN WARNED. Anyways, lets get on with it!

Disclaimer; I do not own. I wish, but no.

"_He didn't give you anything sweetie. Well, not exactly. But, Clary dear, you're pregnant." He explained rather awkwardly._

Clary stared blankly at Magnus while he waited patiently for her to gather herself. Clary couldn't really process what was going on right then. All she knew was that her mother was going to kill her, Luke was going to look at her with his quiet disappointed parent look, and Jace was going to have a heart attack. Then it dawned on her, she was going to have to stop training.

"Magnus…?" She asked quietly.

"What is it biscuit?" he asked with a concerned look on his face. The warlock had known Clary since she was born and of all of Alec's little friends he was the most fond of her.

"Can you tell if my training, has ya know, hurt it..?" she asked in a whisper.

Magnus could see the anguish mixed with love on the young girls face and he couldn't help but go to her to comfort her. Four hundred years allowed for the wisdom he needed to comfort the girl he had watched grow all of her life.

"It's okay, Clary. You haven't hurt it. And, even if you had you didn't do it on purpose, you didn't know. Now, I think you and I need to talk about your next step, because even as a shadowhunter you have options if you want them. I won't tell anyone your secrets." He assured her.

"Magnus, I have to keep it, not it, the baby. I just have to." She said.

"Alright, biscuit. What do you want to do in terms of letting people in on your secret?"

"Can we not tell anyone right now? I need to figure out how to tell Jace. He at least deserves to know before anyone else. Please?" She begged him.

"I already told you, I'll keep this secret. BUT, you need to know that you're about 9 weeks, roughly two months. You have a little time, but not much before your slight frame begins to show." He warned her.

With that Clary showed Magnus out of the room. She sent Alec to go get Jace for her, telling him that she just didn't feel very well. Not even two minutes later Jace poked his head into her room with questioning eyes. Clary prepared herself to lay the best part of her life, because if anyone could pick up on every piece of her mood, it was Jace.

"So, what's the diagnosis?" he asked.

"Um, Magnus thinks I'm dehydrated and have a little bit of the flu, so no more training for a few days." She lied through her teeth.

"Clary, shadowhunters fight through the sickness. You know that. You have to train." He said. Obviously Jace wasn't going to let her out of this easily.

"I can't train Jace." She said just as stubbornly.

"I'll make you until you give me a solid excuse as to why not."

"I just can't!"

"Clary, if you don't want to be a shadowhunter, just tell us." He said looking a little hurt. Of course he would assume that she wanted to resume her normal life.

"That's not it, I just- I can't train right now." She was desperately trying to make up excuses, but she knew she was at the end of her line.

"Clary, if you don't tell me why, I don't care, I will drag you into that room myself every single day." He threatened. Leave it to her boyfriend to be the one who didn't care if she was sick as long as she was able to protect herself.

"Jace-" she started, when Isabelle peeked in the doorway.

"Hey Clary, ready to go get some practice in?" she said interrupting the moment with Jace.

Just as Clary started to reply to Isabelle, Jace did it for her by picking her up and carrying her over his shoulder into the practice room with Isabelle trailing behind. Isabelle shot her a funny look, but Clary was too busy seething to notice. Just as Jace put her down on the floor Clary smacked him across the face and started towards the door.

"Clary!" he yelled, obviously pissed now.

"What." She seethed, not facing him.

"Either tell me, and Isabelle, why you can't continue training and drink a little extra water, or get back over here! You know this is a condition of you living in the Institute." He declared.

"Fine," Clary said. "Jace Herondale. I'm pregnant. That's why I can't train. That's why I'm sick. And that's why you really shouldn't boss me around!" She said to a shocked Isabelle and Jace before storming out of the room. She heard the door open behind her and assumed that Jace was following her to talk. She was wrong. Isabelle knocked on her door and poked her head in just as Clary collapsed on her bed in tears.

"Clare?" Isabelle asked.

"Yea?"

"You wanna talk?"

Clary just shook her head. She wanted time to process, not a screaming match and a fight with her boyfriend and she definitely didn't want to talk. Isabelle understood, she wasn't much of a talker herself so she walked into Clary's room, shut and locked the door and climbed onto the bed to hold the girl that she was starting to see as a sister. Clary was endlessly thankful that Isabelle knew what she needed in that moment.

"I know you don't really want to talk right now, but just listen to me for a sec." Isabelle started, "I know things are really scary right now and everytime that you start to get a hold on things everything changes, and its been that way for the last few years, but I just want you to know that I am behind you 100%. I will kick Jace's ass anytime he says something mean and I will yell at your parents and mine for you so that you don't have to. You're basically my sister now Clare, and with all the bad that's happened these last two years, we need something good. This could be our good."

Clary cried harder into the arms of the last person she thought she would have and cried everything she was feeling out. Just as her eyes dried, there was a knock on the door. Isabelle went to answer it with a glare prepared to send anyone away if Clary asked her to. Unsurprisingly it was Alec coming to ask who broke Jace, because after almost two hours he was still standing in the same spot in the training floor with a shocked look on his face. Isabelle shooed Alec away and waited for Clary to give her a sign as to what she wanted.

"Izzy…. Thank you." Clary said, "I mean it, you're the best. I'm gonna go sit with Jace and try and talk to him I think."

"If you need anything just call." Isabelle said before following Clary out of the room and heading into her own room to give them some privacy.

Sure enough when Clary walked into the practice room Jace was standing in the same spot with a mix of emotions on his face. Clary could see anger (mostly directed at himself), shock, worry, fear, excitement, pain, and confusion without much analyzing of his features. She sat down nearby on a mat and waited for him to register that she was in the room. After about five minutes he moved to join her with a look of fear and love mixed on his face.

"Are you ready to talk?" Clary asked him shyly.

"I think so." He said. "So, we're gonna be parents?"


	3. Chapter 3

First a few side notes: Be forewarned that this story contains City of Heavenly Fire spoilers! So, please please don't complain about them because YOU HAVE BEEN WARNED. Anyways, lets get on with it!

Disclaimer; I do not own. I wish, but no.

"_I think so." He said. "So, we're gonna be parents?"_

Jace was really having a hard time wrapping his head around this new development in his life. His first reaction had been to think that it wasn't his, but Clary wasn't the type of person to sleep around, it took her two years to sleep with him! He then started blaming himself, and to be honest he still kind of was. Obviously, despite his use of condoms, they hadn't had enough protection and logically he knew that, besides not having sex, there wasn't much else that they could have done. Now, he was mostly just scared. Their parents were not going to react well, that much was obvious, but so much could happen between now and the time that the baby came that he was mostly scared of the universe.

"Jace?" Clary called to him.

"Yeah, I'm sorry. I keep getting stuck in my head." He said sheepishly.

"I'm sorry." She said, obviously taking the blame onto herself. Just like always.

"Clary, you can't be sorry. If it's anyone's fault it's mine, I should have been more prepared, but I wasn't and that's okay. We can handle this. Tell me what you know."

" I know, that I'm pregnant. Magnus says roughly nine weeks, but that's really all I know. I'm really scared Jace." She told him with a look on her face that made her look like she was a child.

Jace couldn't help but pull her into his arms and hold her. So, their life wasn't going to pan out exactly how they thought it would, but then again when did it ever? Obviously, a baby was a lot of responsibility, but so was saving the world. Jace was confident that they could handle this, hiding it from their parents for a little while longer was going to be a more difficult task however.

"I don't want to sound insensitive or obtuse, but when are you going to tell our parents?" He asked, needing to figure out some sort of strategy. He worked best with plans.

" Not until I have to…." Clary said. He could see the fear written all over her face. "Maybe Isabelle will do it for me."

"Two things. First, I think we should wait until we get a picture of the baby, one of those things they take through your stomach, and tell them then. At least then they will be slightly distracted. And, second Isabelle is not telling our parents that WE'RE having a baby. We have to show them that we're going to be adults about this." Jace said matter-of-factly to his pregnant, oversensitive, on the verge of a break down girlfriend.

Clary just stared at him incredulously before calling for Isabelle. Jace looked at her confused, until Isabelle came storming into the room pulling him up by the back of his shirt. Jace may be able to defend himself and beat Izzy's ass in training but he wouldn't dare mess with her outside of training. When she wanted to be Izzy was a force to be reckoned with.

"Jonathan Christopher Herondale, I don't know what you did to Clary, but you better apologize! You got her into this mess and you will sure as hell hold her hand through it!" Isabelle threatened him with his full name.

"I don't even know what I did!" he exclaimed.

Jace stared incredulously at Clary as she began to giggle. The noise caused Isabelle to drop Jace's shirt and turn to look at Clary with a confused expression on her face. Isabelle continued to look between Clary and Jace with a calculating expression before she herself burst into laughter. Jace just stood there. He didn't understand what made Clary cry, what made her laugh, or what cause Isabelle to burst into laughter. He had a gut feeling that it was joke that he was in the center of though.

"Anyone care to elaborate on the hilarious joke being told?" Jace asked sarcastically.

"I think Clary was just reminding you who's boss." Izzy stated through a giggle.

Jace rolled his eyes at the girls in his life as he walked over to his girlfriend and pulled her out of the room with him. They had talked a little bit about everything that was going on in their never ending adventure of a life, but there was still a lot to discuss. Primarily what their living situation was going to be, the baby, their finances, marriage, just anything that was going to directly affect the baby. Not that Jace necessarily wanted to get married at 17 but, it wasn't exactly a stigma in shadowhunter culture and they did have a home in Alicante that they would be able to make their own. Jace didn't think Clary would be open to all of that right now, but he kept in the ack burner of his mind.

As they approached Jace's room he saw Magnus down the hallway. Magnus shot them a knowing look and waived before he hightailed it to Alec's room. Clary just followed Jace into his room, shut the door and locked it. Apparently she wanted to have some privacy for this conversation too. Their last few encounters had been very heated, very loud, and very public which was a little embarrassing to Jace. He never lost control, well except when Clary was involved.

"I'm sorry I called Isabelle in there.." Clary started before he waived her off.

"Don't apologize, you didn't do anything wrong. I know you're scared, and so am I, and I should have respected that and made an attempt to comfort you, not scare you further. So, I am sorry."

"Oh, Jace. I love you." Clary said running into his arms.

"I love you too Clare-Bear." He said, even though he knew she hated that name, he was partial to it. He watched as she scrunched up her nose at his use of it though, she was so cute- he hoped their baby looked like her.

"I hope not," she said. "You're much cuter than I am, and if it's a boy he would look awfully dainty if he took after me."

"I didn't realize I said that out loud. But, if it's a girl she'd be the prettiest person on the planet, well after me that is." He said winking at Clary.

"You are so full of yourself Herondale."

"You love it Fray."

Jace watched as Clary walked over to his bed and climbed up to sit next to him. Just by looking at her face he could tell that they were getting ready to have a pretty serious discussion. Clary sighed and laid back resting her hands protectively over their little peanut safely inside of her. Jace took a minute to crawl over beside her and lay his head on her tummy and place little butterfly kisses all over it.

"Hi there, little peanut. I'm your daddy, and even though you kind of surprised us I'm really excited that you're coming. It doesn't matter what you are, boy or girl, I'm gonna love you so much that it'll probably smother you, but you'll always have whatever toys you want or whatever weapons, or anything. I promise. I also promise you'll always be loved and you'll never have to grow up questioning that. Your mom and I are going to be the best mommy and daddy ever, but make sure to remember that I'm your favorite. Okay?"

Jace heard Clary giggling at him and lift up his head to kiss her. He really did think that they were going to be the best parents ever. They thrived under pressure and it only made them fall further in love.

A/N: Alright guys, I know somethings are kind of speeding along really fast but, I'm just trying to make things go in a logical order. Also, thank you to everyone who has favorite and reviewed the story! I love it! See you guys again soon!


	4. Chapter 4

First a few side notes: Be forewarned that this story contains City of Heavenly Fire spoilers! So, please please don't complain about them because YOU HAVE BEEN WARNED. Anyways, lets get on with it!

Disclaimer; I do not own. I wish, but no.

_Jace heard Clary giggling at him and lift up his head to kiss her. He really did think that they were going to be the best parents ever. They thrived under pressure and it only made them fall further in love. _

**Clary POV**

Clary could not believe the way that Jace talked to her stomach. She knew that the baby wasn't even close enough to be being big enough to hear anything, but it was cute how Jace wanted to tell the baby he loved them, that we loved them. She really was in love with him, and somehow she just knew that everything was going to be okay. She climbed out of Jace's bed as he fell asleep and made her way to Alec's room to find Magnus. She knocked when she got there and was greeted by a confused looking Alec at the door. They weren't exactly all that close, but they were working on things since the demon realm.

"Um, can I have a second with Magnus?" Clary asked kind of awkwardly.

"Can it wait? We were um, a little busy." Alec said bashfully.

"Oh!" Clary said with a red face, "I'm sorry. I can wait. Just tell him to stop by my room before he leaves tonight, I have a question about my um, diagnosis."

Alec nodded in affirmation and closed the door. Clary walked back to Jace's room to make sure he was still asleep before she wrote a little note, left the institute and headed off to central park to go on a walk. She really needed a little time to think some more about when and how she wanted to tell people about her new situation before she chickened out and just didn't tell anyone. She also wanted to think about the options laid out before her and Jace.

Obviously it wasn't ideal to be a teenage parent but, her parents had managed, and so did millions of other shadowhunters, right? She wasn't really so much worried about what the community would think, but more likely how her mom and Luke would respond. She hadn't been brought up as a shadowhunter, she was raised like a mundane and in the mundane world teenagers having a child was not exactly a positive thing. Luke would definitely be disappointed in her, and although he would reign in her mother he would most likely give her a lecture that would only make her feel worse than being grounded for a thousand years. Robert and Mayrse were most likely going to be disappointed, but accepting. Clary didn't doubt that when it came down to the wire that her parents would accept their grandchild with open arms and spoil them with love and gifts, but they would not be happy with Clary and Jace for quite a long while.

As if her worries about her parents weren't enough, Clary started to think about their living situation. She knew that she wanted to stay at the institute as long as she was welcomed, but if she wasn't training there wouldn't be any reason for her to be there. She needed to be with Jace through this whole ordeal though. She wanted him involved, and he wanted to be involved, and that required them living together. If she got kicked out of the institute, her parents would never allow Jace to move in with them and stay in Clary's room with her, even if she was already pregnant. They were not liberal parents. Their other option seemed to be moving to Idris and into the Herondale Manor. While having a beautiful home in the country of shadowhunters seemed appealing they would have no family around to help them with their transition into parents. The only family Clary had there was Amatis and she was gone. Maybe, maybe Zachariah would be in the city, but he wasn't the same as their family. It was an option to just move everyone with them into the Herondale Manor, but Clary doubted that anyone would be willing to make the move. So they wouldn't be going there anytime soon.

As she walked in thought Clary felt her phone buzz in her pocket. She looked at the caller ID and saw that Jace was calling her. She answered quickly knowing that he was easily prone to overreacting.

**Jace POV **

Jace didn't realize I had falled asleep until he turned over and heard the crinkling of paper. He looked over and saw a note sitting on my pillow. Since he didn't hear or see Clary in the room he just assumed it was from her.

_Jace,_

_I went for a walk to clear my head. I just need to think about some things. I have my phone if you need me. I'll be back soon. I love you._

_Love you,_

_Clary_

Jace could understand most of Clary's worries, they were mostly his worries too. The only difference between the two of them was that Jace didn't necessarily worry about the outcome of the future, he just knew that it would work out for them in the end. Clary tended to freak out a bit more than he did. He didn't blame her, it was just her personality. He took out his phone and dialed her number just to make sure that she was still okay. He knew that she didn't carry weapons around everywhere she went like the rest of them did, and if she encountered anything nasty she wasn't likely to fight now.

"Hello?" he heard Clary say on the other line.

"Hey, Clare-Bear." He laughed to himself at the use of the nickname that she hated. "I just wanted to make sure you were still okay."

"I'm fine. I just went on a walk Jace. I'm pregnant, not crippled." She said back in her fiery, annoyed voice. Jace chuckled.

"I know that. I'm just making sure you didn't run into anything, get kidnapped, accidentally drown…. You know anything like that." He said innocently.

"I'm fine, I'm heading back now actually, but I'm meeting with Magnus again so I might be a while tonight. I'll find you when I get done, okay?"

"Alright… I love you Clary Fray." He said to her a little disappointed that she wouldn't be back in his arms right away.

"I love you too Jace. Bye."

When she hung up Jace decided to go talk to Izzy and ask her advice on a few ideas he had to surprise Clary. He really wanted to show her that he was ready for this next step in their life and that he was going to stand by her through the whole process. Obviously he couldn't just go out and buy everything they needed for a nursery, but he could get her a baby book or two and maybe even a shadowhunter baby book- if that even existed. Jace knew that shadowhunter births and pregnancies were a little different because of the angel blood in their bodies, but he didn't know if anyone had ever written a book about it. He decided to ask Izzy about, she was a girl, she should know.

"Izzy! Let me in! It's important." He called after he had knocked on her door three times just to get told to go away.

"What?!" she asked as she opened her door in very little clothing and a sheepish looking Simon behind her. He may be human again, have very few memories, and was now ascending into shadowhunter lineage, but that apparently didn't mean that he and Izzy were slowing down any. Jace glared at them.

"Its. About. Clary." Jace said through his clenched teeth.

"Clary?" Isabelle asked.

"Clary," he confirmed. "And peanut." He added.

Isabelle just gave him a funny look but clearly got the message. She sent Simon to go get them something to eat and maybe a drink so that we would have a few minutes to talk alone. She was obviously a little frustrated that I interrupted her and Simon, but she was willing to help in any way I needed her to with peanut and Clary.

"Peanut?" She asked.

"Well I can't name the baby, if I don't know what it is." He said seriously to his sister.

"What do you need Jace?" she replied rolling her eyes.

"I want to get a few things for Clary to show her I'm gonna be right here through the whole thing with her, but I don't know what I can get her this early."

"I have an idea!"

"Shoot. I'm open to options."

"What about an engagement ring!"

I rolled my eyes. "Izzy she isn't ready for that."

"Well, what about something of yours from when you were little? When you first came here you carried around a raggity old blanket and we weren't even allowed to touch any of your things. I mean, I know now that they don't hold much meaning to you with Valentine and all, but they used to be the only memory you had left of your father."

"I'll think about it. Um, hey Iz?" he asked awkwardly.

"Yeah?"

"Do they make like a shadowhunters guide to birth?"

A/N: Okay! So, two chapters tonight! It was my only day off today, so you got a little spoiled, until next time!


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